net.maizegenetics.analysis.gbs.neobio.BasicScoringScheme Maven / Gradle / Ivy

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/*
 * BasicScoringScheme.java
 *
 * Copyright 2003 Sergio Anibal de Carvalho Junior
 *
 * This file is part of NeoBio.
 *
 * NeoBio is free software; you can redistribute it and/or modify it under the terms of
 * the GNU General Public License as published by the Free Software Foundation; either
 * version 2 of the License, or (at your option) any later version.
 *
 * NeoBio is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY;
 * without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
 * PURPOSE. See the GNU General Public License for more details.
 *
 * You should have received a copy of the GNU General Public License along with NeoBio;
 * if not, write to the Free Software Foundation, Inc., 59 Temple Place, Suite 330,
 * Boston, MA 02111-1307, USA.
 *
 * Proper attribution of the author as the source of the software would be appreciated.
 *
 * Sergio Anibal de Carvalho Junior		mailto:[email protected]
 * Department of Computer Science		http://www.dcs.kcl.ac.uk
 * King's College London, UK			http://www.kcl.ac.uk
 *
 * Please visit http://neobio.sourceforge.net
 *
 * This project was supervised by Professor Maxime Crochemore.
 *
 */

package net.maizegenetics.analysis.gbs.neobio;

/**
 * This class implements a basic scoring scheme. At least three parameters must be
 * provided to the constructor: the reward for a match (a substitution of equal
 * characters), the penalty for a mismatch (a substitution of different characters) and
 * the cost of a gap (an insertion or deletion of a character). Note that it only supports
 * an additive gap cost function.
 *
 * Although the match reward is expected to be a positive value, and the mismatch
 * penalty and the gap cost are expected to be negative, no attempt is made to enforce
 * these behaviour.
 *
 * @author Sergio A. de Carvalho Jr.
 */
public class BasicScoringScheme extends ScoringScheme
{
	/**
	 * The reward for a match (a substitution of equal characters).
	 */
	protected int match_reward;

	/**
	 * The penalty for a mismatch (a substitution of different characters).
	 */
	protected int mismatch_penalty;

	/**
	 * The cost of a gap (an insertion or deletion of a character).
	 */
	protected int gap_cost;

	/**
	 * The maximum absolute score that this scoring scheme can return, which is the
	 * maximum absolute value among match_reward,
	 * mismatch_penalty and gap_cost.
	 */
	protected int max_absolute_score;

	/**
	 * Creates a new instance of a basic scoring scheme with the specified values of
	 * match reward, mismatch penalty and gap cost. The case of characters is significant
	 * when subsequently computing their score.
	 *
	 * @param match_reward reward for a substitution of equal characters
	 * @param mismatch_penalty penalty for a substitution of different characters
	 * @param gap_cost cost of an insertion or deletion of any character
	 */
	public BasicScoringScheme (int match_reward, int mismatch_penalty, int gap_cost)
	{
		this (match_reward, mismatch_penalty, gap_cost, true);
	}

	/**
	 * Creates a new instance of basic scoring scheme with the specified values of
	 * match reward, mismatch penalty and gap cost. If case_sensitive is
	 * true, the case of characters is significant when subsequently
	 * computing their score; otherwise the case is ignored.
	 *
	 * @param match_reward reward for a substitution of equal characters
	 * @param mismatch_penalty penalty for a substitution of different characters
	 * @param gap_cost cost of an insertion or deletion of any character
	 * @param case_sensitive true if the case of characters must be
	 * significant, false otherwise
	 */
	public BasicScoringScheme (int match_reward, int mismatch_penalty, int gap_cost,
								boolean case_sensitive)
	{
		super(case_sensitive);

		this.match_reward = match_reward;
		this.mismatch_penalty = mismatch_penalty;
		this.gap_cost = gap_cost;

		// store the maximum absolute score that this scoring scheme can return,
		// which is the maximum absolute value among match_reward, mismatch_penalty
		// and gap_cost
		if (Math.abs(match_reward) >= Math.abs(mismatch_penalty))
			if (Math.abs(match_reward) >= Math.abs(gap_cost))
				this.max_absolute_score = Math.abs(match_reward);
			else
				this.max_absolute_score = Math.abs(gap_cost);
		else
			if (Math.abs(mismatch_penalty) >= Math.abs(gap_cost))
				this.max_absolute_score = Math.abs(mismatch_penalty);
			else
				this.max_absolute_score = Math.abs(gap_cost);
	}

	/**
	 * Returns the score of a substitution of character a for character
	 * b according to this scoring scheme. It is match_reward
	 * if a equals b, mismatch_penalty otherwise.
	 *
	 * @param a first character
	 * @param b second character
	 * @return match_reward if a equals b,
	 * mismatch_penalty otherwise.
	 */
	public int scoreSubstitution (char a, char b)
	{
		if (isCaseSensitive())
			if (a == b)
				return match_reward;
			else
				return mismatch_penalty;
		else
			if (Character.toLowerCase(a) == Character.toLowerCase(b))
				return match_reward;
			else
				return mismatch_penalty;
	}

	/**
	 * Always returns gap_cost for the insertion of any character.
	 *
	 * @param a the character to be inserted
	 * @return gap_cost
	 */
	public int scoreInsertion (char a)
	{
		return gap_cost;
	}

	/**
	 * Always returns gap_cost for the deletion of any character.
	 *
	 * @param a the character to be deleted
	 * @return gap_cost
	 */
	public int scoreDeletion (char a)
	{
		return gap_cost;
	}

	/**
	 * Returns the maximum absolute score that this scoring scheme can return for any
	 * substitution, deletion or insertion, which is the maximum absolute value among
	 * match_reward, mismatch_penalty and
	 * gap_cost.
	 *
	 * @return the maximum absolute value among match_reward,
	 * mismatch_penalty and gap_cost.
	 */
	public int maxAbsoluteScore ()
	{
		return max_absolute_score;
	}

	/**
	 * Tells whether this scoring scheme supports partial matches, which it does not.
	 *
	 * @return always return false
	 */
	public boolean isPartialMatchSupported ()
	{
		return false;
	}

	/**
	 * Returns a String representation of this scoring scheme.
	 *
	 * @return a String representation of this scoring scheme
	 */
	public String toString ()
	{
		return "Basic scoring scheme: match reward = " + match_reward +
		", mismatch penalty = " + mismatch_penalty + ", gap cost = " + gap_cost;
	}
}